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Parliament's Portfolio Committee on Home Affairs says it is "disappointed" that former Home Affairs director general Mkuseli Apleni resigned from his position at such an "unfortunate time".

On Monday, Home Affairs Minister Malusi Gigaba officially announced that Apleni resigned to "pursue other career opportunities in the private sector".

Committee chairperson Hlomani Chauke praised some of Apleni's "achievements", but said the committee was "disappointed" that he had decided to leave the department "while it is in a process of re-invention".

"While the committee acknowledges that departure is inevitable, the resignation of Mr Apleni comes at an unfortunate time," Chauke said on Tuesday.

"The committee is preparing to reflect on some of the department's work, including the Fireblade Aviation issue and the Gupta naturalisation process, which the committee hoped Mr Apleni would have assisted in resolving."

The committee is currently embarking on a two-stage process to probe the events that led to five members of the Gupta family receiving early naturalisation.

Chauke called on Gigaba to expedite the process of appointing a permanent director general to ensure stability, accountability and service delivery.

He praised Apleni for reaching more than 80% of targets, digitising the department's processes and improving financial controls within the department.

'Litany of disasters'

However, DA MP Haniff Hoosen said on Monday that Apleni's resignation would not deter the party from holding him accountable.

"Mr Apleni must know that he will not be absolved for his role in the Gupta naturalisation saga.

"Apleni is right to resign. During his nearly 10-year tenure, he presided over a litany of disasters such as granting several members of the Gupta family citizenship and compromised national security when the Gupta wedding guests landed at the Waterkloof Air Force Base in 2013, among others."

Apleni and Gigaba had also failed to re-open the Refugee Reception Office in Port Elizabeth almost eight years after the Constitutional Court ordered them to do so.

"These inefficiencies at the department have directly contributed in fuelling the illegal immigration crisis in the country," he charged.

While Apleni's resignation was "long overdue", he should also not be scapegoated, Hoosen continued.

"Minister Gigaba himself must follow suit and also resign. With the duo at the helm of DHA (the Department of Home Affairs), services have collapsed and the laws meant to govern and safeguard our country have been severely undermined."

He said his party would continue to call for his appearance in Parliament, for the inquiry due to begin on the Gupta naturalisation issue after the Parliamentary recess in August.

'Reign of terror'

Meanwhile on Monday, unions welcomed Apleni's resignation.

"During his 10-year tenure, Mr Apleni used his authoritarian style of leadership to persecute our members and workers," the National Education, Health and Allied Workers' Union (Nehawu) said in a statement on Monday.

"His departure will relieve our members and workers from his reign of terror in the department which went on unabated for far too long."

The Public Servants' Association (PSA) echoed similar sentiments, accusing Apleni of being "unfit" to head the department.

"Mr Apleni… will unfortunately be remembered by the PSA for especially his [unfair] implementation of weekend working hours without compensation for employees of the Department of Home Affairs," said PSA deputy general manager Tahir Maepa.

Former Home Affairs minister Hlengiwe Mkhize suspended Apleni in September last year.

Apleni, who was appointed to the position in 2010, successfully challenged the suspension in the North Gauteng High Court in Pretoria.

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